{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9151XHFL",
"aliases": [
"buenrostro-bernstein:scRNA Lib 607"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9151XHFL](/measurement-sets/IGVFDS9151XHFL/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS9151XHFL/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9151XHFL](/measurement-sets/IGVFDS9151XHFL/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9151XHFL/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9151XHFL](/measurement-sets/IGVFDS9151XHFL/) has in progress subobject tabular file [IGVFFI9034HUWG](/tabular-files/IGVFFI9034HUWG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9151XHFL/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM1149LLIF](/tissues/IGVFSM1149LLIF/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/tissues/IGVFSM1149LLIF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9151XHFL](/measurement-sets/IGVFDS9151XHFL/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS9151XHFL/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1149LLIF](/tissues/IGVFSM1149LLIF/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/tissues/IGVFSM1149LLIF/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2025-03-09T15:52:05.604266+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9446AKYF/",
"accession": "IGVFDO9446AKYF",
"aliases": [
"buenrostro-bernstein:Donor 2047"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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"accession": "IGVFFI2352SZMI",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:00:03.072374+00:00",
"file_format": "fastq",
"file_size": 8142118212,
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"s3_uri": "s3://igvf-files/2025/03/09/fb716c07-5537-42f1-a5a3-83cf8de71aab/IGVFFI2352SZMI.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
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"upload_status": "validated"
},
{
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],
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"creation_timestamp": "2025-03-09T16:00:04.332304+00:00",
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},
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},
{
"@id": "/sequence-files/IGVFFI4371FJPY/",
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],
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"controlled_access": false,
"creation_timestamp": "2025-03-09T15:59:03.578032+00:00",
"file_format": "fastq",
"file_size": 2327918717,
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"s3_uri": "s3://igvf-files/2025/03/09/ddaa46c7-403a-4524-a00f-42baefdd1c5b/IGVFFI4371FJPY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1914_L8_SS-PKR-432_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8293BFAC/",
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"buenrostro-bernstein:SS-LS_7376_R2"
],
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"creation_timestamp": "2025-03-09T15:59:05.548260+00:00",
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"s3_uri": "s3://igvf-files/2025/03/09/9d6ca505-c7e1-42ad-92bc-e58b36766f53/IGVFFI8293BFAC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1914_L8_SS-PKR-432_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4599BEHH/",
"accession": "IGVFFI4599BEHH",
"aliases": [
"buenrostro-bernstein:SS-LS_5379_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T15:59:47.343030+00:00",
"file_format": "fastq",
"file_size": 8190623055,
"href": "/sequence-files/IGVFFI4599BEHH/@@download/IGVFFI4599BEHH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/b6b0df19-c68a-41a1-a4a4-9443505d0ad2/IGVFFI4599BEHH.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1588_L5_SS-PKR-432_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1179JRYX/",
"accession": "IGVFFI1179JRYX",
"aliases": [
"buenrostro-bernstein:SS-LS_5379_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T15:59:49.300764+00:00",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4515HUNL/",
"accession": "IGVFFI4515HUNL",
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"buenrostro-bernstein:SS-LS_7376_seqspec"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8781PWYP/",
"accession": "IGVFFI8781PWYP",
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"buenrostro-bernstein:SS-LS_5379_seqspec"
],
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},
{
"@id": "/configuration-files/IGVFFI2261FPNI/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7496XAWN/"
],
"lab": {
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"title": "Jason Buenrostro, Broad"
},
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"onlist_files": [
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"preferred_assay_title": "SHARE-seq",
"protocols": [
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{
"@id": "/measurement-sets/IGVFDS3368OEWN/",
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"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:27.432433+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1149LLIF/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1149LLIF",
"aliases": [
"buenrostro-bernstein:BioSam 4965_SS-PKR 432"
],
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"classifications": [
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],
"institutional_certificates": [],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
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"term_name": "brain"
}
],
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"summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 432)",
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}
],
"schema_version": "26",
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"submitted_by": {
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"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "834e9651-1c9f-4c76-94f7-542b1f421935"
}